CoordinationNumber.hpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#ifndef APPLICATIONS_STATICPROPS_COORDINATIONNUMBER_HPP
#define APPLICATIONS_STATICPROPS_COORDINATIONNUMBER_HPP
 
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
using namespace std;
namespace OpenMD {
 
  /**
   * @class CoordinationNumber
   * @brief CoordinationNumber
   *
   * Computes a distribution of coordination numbers defined as the number of
   * atoms in \a sele2 that are within \a rCut of the atom in \a sele1
   *
   * Note that extra parameters must be declared:
   *
   *   \param rCut cutoff radius for finding lists of nearest neighbors
   *   \param sele1 selection of StuntDoubles used for the distribution
   *   \param sele2 selection of StuntDoubles used for nearest neighbor
   * computation
   */
  class CoordinationNumber : public StaticAnalyser {
  public:
    CoordinationNumber(SimInfo* info, const std::string& filename,
                       const std::string& sele1, const std::string& sele2,
                       RealType rCut, int bins);
 
    virtual ~CoordinationNumber() = default;
    virtual void process();
    virtual void writeOutput();
 
  protected:
    virtual RealType computeCoordination(int a, vector<vector<int>> neighbors);
    RealType rCut_;
    int bins_;
 
    std::string sele1_;
    SelectionManager seleMan1_;
    SelectionEvaluator evaluator1_;
 
    std::string sele2_;
    SelectionManager seleMan2_;
    SelectionEvaluator evaluator2_;
 
    int selectionCount1_;
    int selectionCount2_;
    int nnMax_;
    RealType delta_;
    int count_;
    std::vector<RealType> histogram_;
  };
 
  /**
   * @class SCN
   * @brief Secondary Coordinate Number
   *
   * Computes a distribution of secondary coordination numbers where
   * each atom is assigned the mean coordination number of the
   * neighboring atoms.
   */
  class SCN : public CoordinationNumber {
  public:
    SCN(SimInfo* info, const std::string& filename, const std::string& sele1,
        const std::string& sele2, RealType rCut, int bins);
 
    virtual RealType computeCoordination(int a, vector<vector<int>> neighbors);
  };
 
  /**
   * @class GCN
   * @brief Generalized Coordinate Number
   *
   * Computes a distribution of generalized coordinate numbers as
   * described in:
   *
   *   "Finding optimal surface sites on heterogeneous catalysts by
   *    counting nearest neighbors," by F. Calle-Vallejo et al.,
   *    Science 350(6257) pp. 185-189 (2015).
   *    http://dx.doi.org/10.1126/science.aab3501
   */
  class GCN : public CoordinationNumber {
  public:
    GCN(SimInfo* info, const std::string& filename, const std::string& sele1,
        const std::string& sele2, RealType rCut, int bins);
 
    virtual RealType computeCoordination(int a, vector<vector<int>> neighbors);
  };
}  // namespace OpenMD
 
#endif